


We met as Enemies, Left as Lovers

by IdrisTheTardis



Series: Star Trek Kink Meme Fills [3]
Category: Star Trek: Alternate Original Series (Movies), Star Trek: The Original Series
Genre: 5+1 Things, Alternate Universe - Canon Divergence, BAMF Enterprise Crew, Embarrassed Khan, Khan is totally crushing, M/M, Slash, but that's okay cause Jim is too
Language: English
Status: Completed
Published: 2014-07-09
Updated: 2014-07-15
Packaged: 2018-02-08 02:16:04
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings, No Archive Warnings Apply
Chapters: 2
Words: 4,726
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1922955
Author URL: https://archiveofourown.org/users/IdrisTheTardis/pseuds/IdrisTheTardis
Summary: <blockquote class="userstuff">
              <p>Written for a prompt on the Star Trek into Darkness Kink Meme:</p>
<p>The Augments never lost control over Earth. Even three hundred years later they are still in power. That doesn't mean humans ever stopped rebelling.</p>
<p>Kirk and the rest of the crew are part of the dwindling resistance and the net is closing around them. To get away they commandeer one of the augments new ships (the Enterprise) and flee into space. </p>
<p>Khan is the captain of the ship sent after them. There are two possible paths author can go from this point:</p>
<p>1) Khan captures the Enterprise. Kirk tries to convince him that it was all his doing and he had tricked the crew into going along with it to try to get them lighter sentences. Khan knows better but is impressed by the captain who would so quickly lay down his life for his crew.</p>
<p>2) The Enterprise is able to avoid capture though there are quite a few close calls. Khan gradually begins to fall for the man that has been able to escape from seemingly impossible situations and Kirk falls for the man that would chase him to the end of all space.<br/>(http://strek-id-kink.livejournal.com/2836.html?thread=872212#t872212)</p>
            </blockquote>





	1. The Chase

The first time Khan sees Jim Kirk - member of the futile human rebellion against the superior Augment's Empire, thief, hacker, and basically all around criminal extraordinaire and constant thorn in the side of Khan's superiors - is in a shopping centre's food court. He isn't sure at first that it is really him, until Pavel Chekov - child genius, responsible for taking down the Empire's subspace communications network for more than a week before being discovered and stopped - sits down at the table with him and hands him fries and a coke. It's strangely surreal he reflects as he watches them be taken into custody, that two of the most dangerous and sought after rebels would be caught over fast food. His Captain is too busy celebrating the promotion he is now assured to get to question their good fortune to question anything. Khan decides that he will be keeping a close eye on Kirk and Chekov until they have been transferred to the holding cells on Empire Base 12.

<><><>

The second time Khan sees Jim Kirk is in the detainment centre aboard the Enterprise, only hours after the first time. Khan is there with his Captain, who had come to the decision that he did not wish to leave their interrogation for the Base. Kirk and Chekov have been placed in different cells, out of view of each other, and yet neither of them seems to be concerned about the situation they have found themselves in. Khan once again got the feeling that there was more going on than he was able to see. The Captain immediately starts asking Kirk questions about their purpose on Risa, and the rebels plan for the Gamma 400 system in general, throwing in mocking comments about their easy capture and what it said about the state of the rebellion. Kirk remained calm and unaffected by the mocking and questions. He merely smirked and responded flippantly, "oh don't you worry, you'll know it when you see it."  
  
This only served to infuriate the Captain, who continued demanding questions, moving on from mocking to threatening to torture Kirk for the answers he sought. Kirk only responded with further condescending and sarcastic remarks to all of the Captain's questions. They are enough to burst the bubble of happiness the Captain has from capturing them and send him storming out of the room, but not before making a snide remark about what awaited the 'pretty' pair when they reached the penal planet they would inevitably be sent to. Unlike the threats of torture, this causes Kirk to tense, and Khan pauses a moment, contemplating what it was that made the threat of rape worse to Kirk than the threat of torture at the experienced hands of Empire interrogators. Kirk ignores his presence, his eyes focused on the wall that blocks his view of Chekov's cell, and Khan understands. He turns and leaves, walking past Chekov without looking at him, trying and yet unable to stop himself from sympathizing with a man who mirrors his feelings for his crew so perfectly.

<><><>

The third time Khan sees Jim Kirk, it is not in person, but on a viewscreen while he is at Base 12 and Kirk is flying away in the newly stolen Enterprise, along with any dream the Captain has of receiving a promotion or even staying Captain. At the time he does not know that the Enterprise, Flagship of the Empire, was lost because the Captain had the entirety of the crew not on shore leave, with the exception of the crew member responsible for manning the transporter, beam over to the Valiant to search the ship after Kirk and Chekov escape and manage to somehow intimidate the crew into abandoning the ship, only to have them transport themselves onto the Enterprise and overpower that crewman, and after sending him over to the severely crippled Valiant, flying away. They stop just outside of range of Base 12's defensives to call the base and tell them that they should blame the Captain personally for the bug that they had also installed into the Base's system as they had not planned on installing it until the Captain' comments on what their fates would be in prison. Upon hearing this, Khan corrects his thought from earlier to the Captain giving up any dream of being allowed to stay in the service at all. He ignores the admiration he feels towards Kirk for such impressive revenge.

<><><>

The fourth time Khan sees Jim Kirk is almost a year after the last time he had seen him. Khan had spent that year following Ji- **Kirk** across the Galaxy, trying and failing to capture Jim and any member of his merry band of misfits, while also failing to stop the majority of the trouble they brought with them to the Empire wherever they went. Despite several close calls, Khan manages to continually miss J- _ **Kirk**_ , though he does meet and temporally arrest several members of Jim's crew, from Spock - the half-bred, emotionless genius who is able to effortlessly beat many Augment in hand-to-hand combat- to 'Bones' - the doctor who discovered how to fake testing positive to being a Augment - to… Nyota Uhura (?) - a xenolinguistics expert able to speak any language and impersonate any member of the Empire, whether male, female, or other-.  
  
None of them show fear when they are captured, all sure at they will be rescued before anything too bad happens to them. Instead of fear they all seem to be amused when they meet him, smirking and making comments as though they know something he does not. No one is really sure how it is they escape, they merely disappear from their cells and the ship altogether the second the guard moves away. As such, when after a year Khan finally manages to apprehend Kirk after a year of chasing him, he doesn't truly expect to hold on to him for more than a few hours at most. A great overestimation of his crew's abilities against the rebels apparently, seeing as how Kirk does not even make it to his cell before he escapes. Khan had trouble stopping himself from questioning call these people inferior for being human when their skills are obviously far superior to many of the officers he has served with.

<><><>

 Khan is not sure if the fifth time he sees Jim Kirk was real or simply a hallucination brought on from blood loss. He likes to think it was real, that Jim - he's not sure when Kirk had become Jim in his mind, but cannot find it in himself to care too deeply - had been there and had saved him from an impossible situation that even his crew could not save him from. But for all his skills at evading capture and wreaking havoc, Khan cannot see how Jim would have found him on an uninhabited planet, nowhere near any settled planet. And even if he has, Jim has no reason to have helped him, the person burdened with the responsibility to catch him and reclaim the Enterprise. It would, in fact, be in Jim's best interest to leave him to die. His thoughts, after all, are not hindered by the respect, admiration, and… other emotions that Khan has for him and is unable to stop from growing each time he and Jim come head-to-head. Khan can't help but hope that it really had been Jim who saved him.


	2. The Capture

**Notes for the Chapter:**

> This did not turn out how I thought it would. Guess that's what I get for doing all my writing at 3 in the morning.

"Oh, hi guys, need a hand?"  
  


Khan spares only a moment to wish that he could disappear into a deep, deep hole before turning his full attention to the image on the viewscreen. "Kirk," he says, acknowledging the man who has haunted his days and nights for almost the past two years.  
  


"Oh come on Khan," the rebel wines, somehow managing to slouch further into the captain's chair, "we just saved your ship from being completely destroyed, the least you could do is call me **Captain** Kirk. Or Jim," he adds after a moment of thought, "you could definitely call me Jim. You didn't seem to have a problem calling me that last time we meet."  
  


Khan suppressesa blush while trying and failing to ignore the confused, and in some cases amused, looks being shot at him by all of his crew. Kati, the traitor, smirks at him. "I thought he was a hallucination," he hisses at them.  
  


"What, really?" Jim asks, sitting up with a smirk of his own on his face. "You mean you don't remember when I-"  
  
Khan knows Jim well enough to not let him finish, "Captain Kirk, would you please explain why you interfered with the Gorn's attempt to destroy our ship?"  
  


If possible, Jim's smirk grows wider, "well we couldn't just sit back and allow them to kill our favourite Empire Captain and crew. I mean, who would chase us around the Galaxy if something happened to you guys?"  
  


Khan's eye's flick to where Spock stands behind Jim, "that is the most illogical thing I have ever heard."  
  
Jim waves this off, "oh you know you love us. How could you not after the birthday card we sent you?"

  
Khan raises an unimpressed eyebrow at him, "and by birthday card, you are referring to the crayon drawings you made on the Empire's constitution?"  
  
"That's the one!" Jim beams at him, "don't pretend you didn't love it, I know you did." Khan doesn’t reply and Jim just continues smiling at him for a moment before settling his face into a more serious expression. "Now, as fun as this conversation is, I think we should continue it later. Right now we need to talk about you and your crew's surrender."  
  


"That will be a very short conversation," Khan replied coolly, "we refuse to surrender."  
  


Jim's expression is blank. "Let's not play games, Khan. We know you dilithium crystals have been severelydamaged. You won't be able to travel any real distance before your warp core fails completely, which will leave you drifting in enemy space. How long, Spock, do you think it will take them to be found by another Gorn ship? Or even a Tholian ship?"  
  
Spock’s voice is just as emotionless as his. "I estimate it should take no more than five hours before they are found and destroyed, Captain."  
  


Khan hates to admit it, but he knows they are right. They are light years away from the nearest Empire base, which is just an unmanned mining station, and their long range communications were knocked out at the beginning of the fight. And, given just how many of the Empire's enemies are known to hide in this sector, five hours is a rather optimistic life span. His eyes move to McGivers, and he knows she has come to the same conclusion as he has. "Very well, it seems we have no choice. We surrender."  
  


Jim nods decisively. "Good. Turn off your engines and lower your shields. You, along with your crew members: Joachim, Joaquin, Kati, McGivers, and Rodriguez, will be beamed over to the Enterprise to ensure that the rest of your crew does not attempt to attack us before we reach our destination. Once you are aboard, we will commence towing the Vengeance. Is that understood?"  
  


Khan can't help but wonder why Jim thinks it will be safer to have six Augments on his ship than to just destroy them should they try to fight, but he is not going to question an order that might lead to them being able to retake the Enterprise. That would let him regain at least a small part of his dignity that he lost by having to be saved by Jim not once, but twice. In less than half a year. His family will be so disappointed in him when they hear. "It is," he acknowledges before ordering his crew, "McPherson, turn the engines off. Otto to lower the shields. Joachim, please comm Joaquin and inform him his presence is required on the bridge."  
  


There is silence as they wait for Joaquin to arrive. When he does, he moves to stand by Khan and Marla, with Kati, Joachim, and Rodriguez move as well. He stands and nods to Jim's image. "We are ready."  
  
Jim nods, saying "beam them over, Scotty."  
  


<><><>   
  


They appear in the Enterprise only for them all to be immediately stabbed with needles. They stagger as the contents of the needles enter into their blood. "What have you given us?" Khan demands, voice weak.  
  
"Calm down Princess, you'll be fine," is the gruff response he gets from the man who had given him his needle. "Just a little cocktail to make sure you and your people don't try to kill us all. I would hate to have to listen to Spock telling Jim 'I told you so' for the rest of my indubitably short lifetime."  
 

Khan, having recovered his bearings, turns to look at the man speaking and is met with Jim's medical officer, 'Bones'. "And what is in this cocktail, Doctor?"  
  


"Like I'd tell you," he scoffs.  
  


Khan opens his mouth to respond but is interrupted by the opening of the door, allowing Jim to enter the room, accompanied by Spock. Turning towards them, he demands, "Captain Kirk, I would like to know what it is that you have had my crew and I injected with."  
  


Instead of answering Khan's question he turned to scowl at his Officer. "Bones."  
  


"Damn it Jim, I'm not going to allow six Augments to walk around at full power. It's suicide."  
  


Jim rolled his eyes, but turned back to Khan, "I apologize on behalf of my medical officer. You were injected with Kryptonite. I believe you should know what that is." Khan does know. Named after some ancient human legend, Kryptonite slows down the body's functions to that of a human. A weak human at that. The rebels had started using it four years ago on every prisoner that they captured, due to its ease of being administrated. It could effectively be given to an Augment through contact, injected, inhalation, or by being eaten by said Augment. The Empire had no idea what was in it or how to counteract it.  
  
Khan nodded, "indeed we do."  
  
Jim stared at him for a moment before clearing his throat and say, "right, well if you would come with us, we can show you to your rooms."  
  
Khan visually startles, "rooms?"  
  


It is Spock, not Jim who responds. "We were unaware if your female crew members would feel comfortable sleeping in the same room as the males so we set up two rooms that connect through a washroom."  
  


"I believe," Marla injected quickly, "that the Captain's query was more about us not being put into cells than about having multiple rooms."  
  


Jim smiled at her as he explained, "we have several days' worth of travel before we reach our nearest base and can hand you off to be traded back to the Empire. As such, we felt that you would be more comfortable in rooms then in cells. After all, they might look fun, but after the first few hours the novelty wears off and then you spend the rest of the voyage bored as hell. This way we avoid at least some of the boredom. Plus," he says with a shrug, "we can always move you to cells later if you cause too much trouble." No, Khan did not want to have her kicked out of the Service for asking that question before he could and stealing Jim's smile that should have been for him. Why would anyone think that?  
  


<><><>   
  


They spend the rest of the day and the next morning debating what their plan of action should be.  
  


"We can't just sit around doing nothing!" Rodriguez states for what feels like the hundredth time.

 

"There is nothing we can do," Marla all but yells. "Our ship can't fly, has no weapons, and no communications. It barely has shields, and yet you think we'll be able to fight our way away from the Enterprise with all dying?"

 

"So we take the Enterprise!"

 

"We have been over this Rodriguez," Khan says, unable to stand another minute listening to them argue back and forth about topics they had already covered. "We cannot take Enterprise when we are under the effects of Kryptonite and as it can easily be made into a colourless, scentless

 gas, we are most likely breathing it in as we speak and will continue to do so for the remainder of the voyage."

 

"We could still try."

 

"And if we succeeded?" Joaquin asked, "what then? We have no idea what changes have been made to this ship since the rebels stole it. We can't even be certain that we would be able to start it, let alone fly it."

 

"We have nothing to gain from fighting," Kati says, using her most rational tone of voice. "They have not hurt us, they have not threatened us. They have tried to keep us comfortable and allowed us together to stop our boredom. This will change if we act out. We do not know how long we will be on this ship, it is best not to anger the ones in charge."

 

" **We** have nothing to gain," Joachim stresses, and Khan pretends he doesn't understand what he means and doesn't feel the eyes of his crew on him. He knows what his fate will be when they are returned to the Empire and there is no action they can take to change it. He was saved having to listen to this argument again by the door opening. Jim entered, followed by… Sulu? Yes, he is Sulu - aka Crazy Sword Guy, he once beat twenty Augments with phasers with nothing but his sword and two throwing knives - Khan recognizes him from one of their many close calls with catching the Enterprise and her crew before they managed to wreak havoc.  
 

"Can we help, Captain?" He asks, his crew having fallen silent as soon as the door started to open.

 

"I was wondering if I could have a word with you, Khan," he asks before looking over Khan's shoulder towards his crew, "in private."

 

He takes a moment to think about whether he really wants to be in a room alone with Jim - oh god yes - before answering, "very well." He stands and follows Jim out the door with Sulu following behind them. Jim nods at the two security officers standing outside the door before heading for a door just down the hallway. He opens it and allows Khan to enter first before following him inside. Sulu stays outside guarding the door. "What is it you wished to talk about, Captain?" Khan asks as soon as the door is closed.

 

Jim sighed and sat down in a pink, squishy chair, "You, I wasn't kidding when I said you should call me Jim. And please, sit."

 

Khan frowned at him as he moved to perch on the edge of a bright green and orange chair shaped like a frog, it was the best of a very bad lot. "I understand that you were not kidding Captain."

 

"Riiigth," Jim drawled, "mind telling me then why you won't call me Jim?"

 

"Is this what you wished to talk about?" Khan asked. They stared at each other for several moments, Jim with his eyebrows raised before Khan gave in, "fine, fine. Is this what you wanted to talk about, **_Jim_**."

 

Jim sat up straighter in his chair, the smile he had gained at Khan's use of his name falling away as he started talking. "No, it's not. I actually… Well, I… I wanted to apologize."  
  
Khan stared at him while he tried to process what he had just said. "You want to apologize… To me?" He didn't mean for it to come out as a question but, he isn't sure that he properly understood what Jim had said.

 

"Look, ok, I know that I've been the cause of a lot of problems in your life over the past years. What with the constantly avoiding you, and breaking my people out of your ship faster than you can catch them, and the birthday card, and now, with you being captured…" Jim seems to realize that he's rambling, and stops talking so he can collect his thoughts. Khan lets him as he's not really sure what to say. What do you say to the enemy of state who you've been chasing for almost two years and who you may or may not have a tiny crush on, when he apologizes to you for causing you trouble even though that's his job? "What I'm trying to say is, I know I've caused a lot of trouble that you've been blamed for because you couldn't stop me. And I know that what's happening now, you, your ship, and your entire crew being taken captive, I know that's going to completely destroy what is left of your career. And I'm sorry for that."

 

"You do realize that you are apologizing to the man who has been trying to you almost exactly what you are doing to me, do you not?"

 

Jim shook his head at that comparison, "It's not the same thing. If you had of captured us, we still could have escaped. Your career is over whether you escape or not. And it's not just that. If you hadn't had the misfortune of being assigned to catch us, you probably would have been promoted at least twice over the last two years."

 

Khan shrugs, "I would not have taken them."

 

Jim pauses in his tirade of guilt, frowning at him, "you wouldn't have? Why not?"

 

"Captain is the highest rank you can receive on a ship," He says, his eyebrows raised to express his surprise that he needs to explain this to Jim of all people, "I would not take a promotion to would take me away from my ship, and therefore my crew. They are the truest family I could hope for."

 

This just seems to upset Jim more. "So what you're saying is that not only did I end your career, I'm also responsible for you losing your family."

 

"They will not be lost, they will merely be… gone for a while," Khan says, trying to make Jim feel less guilty. "That is, those who stay in the service. I doubt that I will be the only one to lose my position for the destruction of the newest and most expensive ship in the fleet."

 

"Got any idea what you'll do?" Jim asked.

 

Khan shrugged, not having really thought about it as of yet. "Perhaps I will become an engineer. That is what I studied in university."

 

Jim snorts, "You should talk to Scotty then. He lives for engineering. I think if it was possible he would marry the Enterprise he loves it so much."

 

"And you?" Khan asked, "would you not fight him for the Enterprise? You seemed fairly worried for her whenever she was damaged."

 

"Na, there are some pairs that are just meant to be. Scotty and the Enterprise is one of them. Spock and Uhura, you know who Uhura is right?" he asks, continuing at Khan's nod, "they're another. Whenever we're at a new base, she has guys hitting on her left and right and Spock will just do his 'Violence is seriously fucking nigh" face and they just scatter and she's just like, 'what took you so long, do you know how long I've been waiting?' It's hilarious, it really is."

 

"I will take your word for it."  
  
"What about you," Jim asked, "any couples in your crew who just don't seem right by themselves?"

 

Khan takes a moment to think about his response before saying, "no, not as of yet. However we have not been together as a crew for as long as yours has."

 

Jim nodded in agreement looking at Khan through the corner of his eye as he turned to look around the room, "true, it does take some people a lot longer to find their star crossed lover than others."

 

Khan allows himself to smile at that before responding, "and of course, sometimes you do not find that person where you would expect to find them."

 

Jim turned back towards him with an answering smile, "too true." Jim opens his mouth to say more but is interrupted by Sulu entering the room before he has a chance.

 

"Captain, your presence is needed onboard the bridge."

 

Jim instantly snaps out of his 'friendly, person Jim' into his 'in control, Captain Jim' as he nods. "Very well inform them I am on my way, and then please bring Khan back to his crew.

 

"Yes Captain."

 

Khan watches Jim walk away and most definitely does not think about what their conversation could have turned into if they had not been interrupted.

 

<><><> 

 

"And you're sure you aren't leaving anything out?"

 

"Yes, Joachim."

 

"One hundred percent?"

 

"Yes."

 

"Abs-"

 

"Joachim," Marla snapped, "why do you keep asking if you are not going to believe the answer?"

 

"Oh like you're not having just as hard a time accepting all he wanted to do was _apologize_ as I am."  
  
"No, I am not. Because I actually read the reports that they send out every time the Rebellion manages to capture and ransom someone and as such I know that they do not torture their prisoners."  
  
"Just because they say something-" Khan decides it is in the best interest of his sanity and Joachim's continual life if he stops listening to them argue.

 

<><><> 

 

Jim comes to talk with him again later the next day, after the third meal of the day has been served. Khan, who has spent the last thirty something hours listening to the same two arguments over and over again welcomes the chance to escape to somewhere he won't be able to hear them. He would feel bad, but by now even Kati's patience had started to crack.

 

Of course, he and Jim don't do all that much talking, the door had barely closed behind Jim before he was pushing Khan against the wall and kissing him like his life depended on it. The kiss is hot and hard, their tongues fighting for dominance of Khan's mouth. Jim wins, and proceeds to map out Khan's mouth until they have to pull apart for breath. Khan rests his head on Jim shoulder, turning his nose into Jims throat. Jim is warm and his cologne makes him smell like he just hiked through a pine forest. There's something else in there as well that Khan can't identify, something unique to Jim, but it makes him have to hold back a moan at the mixture of smells.

 

He doesn't do a good enough job holding it back, apparently because Jim groans, and then pulls his face back up to his with one hand while the other started working its way up Khan's shirt. Jim's fingers have just reached Khan's nipple when the door opens and the two of them hastily pull apart. Uhura stands in the door way, smirking at the two of them. "Captain, Commander Spock requested I inform you that we are about to reach base four echo Juliet."

 

Jim cleared his throat and finished smoothing down his uniform. "Yes, thank you, Lieutenant Uhura. Please Inform Commander Spock that I received his message and will join him in the Bridge after I return Khan to his crew,"

 

She continues smirking at them, "of course Captain. Would you like me to come and remind you, should you not be at the bridge in ten minutes?"

 

"That will not be necessary, thank you Lieutenant."

 

"You're welcome, Sir." She salutes and leaves, and Jim leans forward to bang his head on the wall.

 

"She is never going to let me forget this."

 

"Do you wish to?"

 

Jim stops banging his head against the wall and turns to look Khan. "No, I don't. Do you?"

 

"I… would not be averse to continuing what we were doing at a later date. Should we have the chance."

 

Jim smirked at him, "Oh, we'll have the chance. After all, you spent almost two years of your life following me, it's only fair that I return the favour."

 

Khan smirks back at him, "oh, of course. After all, we must be fair."

**Author's Note:**

> Sorry about the lack of dialogue, there will hopefully be more in the next part, which should be updated by next Tuesday. Every comment and/or kudos is appreciated.


End file.
